Yep the SH3 engine is only single threaded, it only uses one core.
But that CPU is fine for playing SH3, a 2ghz Core cpu is actually faster han a 3ghz p4 (I assume that was what you had?)
I have a 2ghz core 2 duo (T7200) and SH3 runs great.
Could be a problem with your new ram? Try downloading a ram tester, you can do a quick and dirty test with the windows one here:
http://hcidesign.com/memtest/
If it finds any errors then you definitely have a problem... but to 100% rule out ram problems you should download one that you burn to a CD and boot from.